# There has been an outbreak of cholerae in Haiti in the last week amongst the people already affected by the earthquake. [http://www.pih.org/news/entry/cholera-in-haiti-another-disease-of-poverty-in-a-traumatized-land/ For example, see the story by Partners in Health.] How, specifically, do you think that research like that we are doing this week can contribute to an improvement in publich health? What do you think the barriers are for this research to lead to viable treatments that can reach the people in Haiti?

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# Next week we will be selecting the teams for the class final projects. What qualities do you look for in a good teammate? What are some of the things that make or break a team project?

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Revision as of 20:55, 25 October 2010

BIOL/CMSI 367-01/HNRS 398-05: Biological Databases

This is the home page for the Fall 2010 Biological Databases course at Loyola Marymount University while the computer science server is down.

Update 10/25/10: The course wiki is partially back up. The wiki pages themselves are available, but any files that were uploaded are not. We will continue to use the OpenWetware wiki for the week of 10/25/10.

In addition, microarray data can sometimes be found as supplementary information with a journal article or on an investigator's own web site.

Calculate the ratio of red/green fluorescence

Log2 transform the ratios

Normalize the log ratios on each microarray slide

Normalize the log ratios for a set of slides in an experiment

Perform statistical analysis on the log ratios

Compare individual genes with known data

Look for patterns (expression profiles) in the data (many programs are available to do this; we won't be doing this in class)

Perform Gene Ontology term enrichment analysis (we will use MAPPFinder for this)

Map onto biological pathways (we will use GenMAPP for this)

Individual Journal Assignment

This journal entry is due on Monday, October 18 at midnight PDT (Sunday night/Monday morning). NOTE that the OpenWetware server records the time as Eastern Daylight Time (EDT), unlike the LMU CS server which was on Greenwich Mean Time (GMT). Therefore, midnight will register as 03:00.

Store this journal entry as "username Week 7" (i.e., this is the text to place between the square brackets when you link to this page).

Create the following set of links.

Link to your journal entry from your user page.

Link back from your journal entry to your user page.

Link to this assignment from your journal entry.

Add the "BIOL367/F10" category to the end of your wiki page.

Preparation for Next Week's Journal Club

In preparation for the Journal Club, each individual will do the following assignment on their individual "username Week 7" pages.

Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries. Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources.

Write an outline of the article. The length should be the equivalent of 2 pages of standard 8 1/2 by 11 inch paper. Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article.

What is the main result presented in this paper? (Hint: look at the last sentence of the introduction and restate it in plain English.)

What is the importance or significance of this work?

What were the limitations in previous studies that led them to perform this work?

What were the methods used in the study?

Briefly state the result shown in each of the figures and tables.

How do the results of this study compare to the results of previous studies (See Discussion).

Upload your completed PowerPoint slides to your journal page by the Week 7 journal deadline (you may make changes before your presentation Tuesday afternoon, but we will be evaluating the presentation you upload.)

For your PowerPoint presentation, you need to show each of the figures and tables in your article as part of your presentation. Do not have a separate section of your presentation for Methods. Instead, show each of the results (figures/tables) and just explain the methods used to obtain those results on that slide.

Week 8 In-class Exercise and Journal Assignment

Analysis of Vibrio cholerae Microarray Data Part 1

For the next section of the course, you will be introduced to the process we will use for the final projects in the course in a series of in-class and journal assignments where we will first analyze microarray data from Vibrio cholerae, and then learn how to create a Gene Database for this organism.

Groups

Rich Brous, Salomon Garcia

Claudia Campos, Andrew Herman

Margie Doyle, Theresa Graebener

Andrew Forney, Zeb Russo

Evan Montz, Jennifer Okonta

Individual Journal Assignment

This journal entry is due on Monday, October 25 at midnight PDT (Sunday night/Monday morning). NOTE that the OpenWetware server records the time as Eastern Daylight Time (EDT), unlike the LMU CS server which was on Greenwich Mean Time (GMT). Therefore, midnight will register as 03:00.

Store this journal entry as "username Week 8" (i.e., this is the text to place between the square brackets when you link to this page).

Create the following set of links.

Link to your journal entry from your user page.

Link back from your journal entry to your user page.

Link to this assignment from your journal entry.

Add the "BIOL367/F10" category to the end of your wiki page.

Keep an "electronic lab notebook", containing your methods, results, and interpretations of this week's portion of the Analysis of Vibrio cholerae microarray data project in your "username Week 8" journal page. Although you will have assigned partner(s), you will need to fill out your own individual journal page.

Be sure to answer any questions embedded in the protocol in your journal page.

Sign your portion of the journal with the standard wiki signature shortcut (~~~~).

Add the "BIOL367/F10" category to the end of the wiki page (if someone has not already done so).

Reflection

What was your initial comfort level with Excel before performing this exercise? Did your comfort level change? Why or why not?

What advice would you give next year's class when performing this assignment?

Do you think the original authors of the Merrell et al. (2002) paper adequately discussed their methods and results of their data analysis in their Nature paper? Why or why not?

Week 9 In-class Exercise and Journal Assignment

Analysis of Vibrio cholerae Microarray Data Part 2

For the next section of the course, you will be introduced to the process we will use for the final projects in the course in a series of in-class and journal assignments where we will first analyze microarray data from Vibrio cholerae, and then learn how to create a Gene Database for this organism.

Individual Journal Assignment

This journal entry is due on Monday, November 1 at midnight PDT (Sunday night/Monday morning). NOTE that the OpenWetware server records the time as Eastern Daylight Time (EDT), unlike the LMU CS server which was on Greenwich Mean Time (GMT). Therefore, midnight will register as 03:00.

Store this journal entry as "username Week 9" (i.e., this is the text to place between the square brackets when you link to this page).

Create the following set of links.

Link to your journal entry from your user page.

Link back from your journal entry to your user page.

Link to this assignment from your journal entry.

Add the "BIOL367/F10" category to the end of your wiki page.

Keep an "electronic lab notebook", containing your methods, results, and interpretations of this week's portion of the Analysis of Vibrio cholerae microarray data project in your "username Week 9" journal page. Although you will have assigned partner(s), you will need to fill out your own individual journal page.

Be sure to answer any questions embedded in the protocol in your journal page.

Note that the OpenWetware wiki will not accept the upload of certain file types the GenMAPP and MAPPFinder will create. To upload these files, you will need to compress them into a .zip file, which will be accepted by this wiki.

The Windows machines in the Seaver 120 computer lab have an evaluation version of WinZip installed that can compress files.

If you are using your own Windows machine and it does not already have a program installed to compress files, the free software, 7-zip, can be downloaded and installed for you to use.

Groups

For this week, we are not going to require a face-to-face meeting of the group. However, we do strongly encourage it.

Sign your portion of the journal with the standard wiki signature shortcut (~~~~).

Add the "BIOL367/F10" category to the end of the wiki page (if someone has not already done so).

Reflection

There has been an outbreak of cholerae in Haiti in the last week amongst the people already affected by the earthquake. For example, see the story by Partners in Health. How, specifically, do you think that research like that we are doing this week can contribute to an improvement in publich health? What do you think the barriers are for this research to lead to viable treatments that can reach the people in Haiti?

Next week we will be selecting the teams for the class final projects. What qualities do you look for in a good teammate? What are some of the things that make or break a team project?